ATACseqQC

ATACseqQC is a Bioconductor package developed for generating diagnostic plots and preprocessing aligned ATAC-seq data for subsequent peak calling. This package provides a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets, and includes guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset.

Topic

Sequencing;Sequence analysis;DNA packaging

Detail

  • Operation: Gene regulatory network analysis

  • Software interface: Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.22.0

  • Credit: The Department of Molecular, Cell and Cancer Biology at UMass Medical School.

  • Input: -

  • Output: -

  • Contact: jianhong.ou@duke.com

  • Collection: -

  • Maturity: Stable

Publications

  • ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
  • Ou J, et al. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data. 2018; 19:169. doi: 10.1186/s12864-018-4559-3
  • https://doi.org/10.1186/s12864-018-4559-3
  • PMID: 29490630
  • PMC: PMC5831847

Download and documentation

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